On 4/12/18 2:55 AM, za...@tezu.ernet.in wrote:
Dear Mark
Thank you for the kind response.
H with +0.418 charge and N with -0.845 charge is contributing towards
coulomb 14 interaction. So what is the amount of interaction between one
single H and N (3 bonds apart)? Kindly correct me if I am wrong.
Simply calculate it with Coulomb's Law and apply the 1-4 electrostatic
scaling factor (if your force field uses one).
-Justin
Here is my Gdm topology
[ moleculetype ]
; name nrexcl
GDM 3
[ atoms ]
; nr type resnr residu atom cgnr charge MASS
1 C 1 GND C1 1 1.027 13.019
2 NT 1 GND N2 2 -0.845 14.0067
3 H 1 GND H3 2 0.418 1.008
4 H 1 GND H4 2 0.418 1.008
5 NT 1 GND N5 3 -0.845 14.0067
6 H 1 GND H6 3 0.418 1.008
7 H 1 GND H7 3 0.418 1.008
8 NT 1 GND N8 4 -0.845 14.0067
9 H 1 GND H9 4 0.418 1.008
10 H 1 GND H10 4 0.418 1.008
[ bonds ]
1 2 2 0.1340 1.0500e+07
1 5 2 0.1340 1.0500e+07
1 8 2 0.1340 1.0500e+07
2 3 2 0.1000 1.8700e+07
2 4 2 0.1000 1.8700e+07
5 6 2 0.1000 1.8700e+07
5 7 2 0.1000 1.8700e+07
8 9 2 0.1000 1.8700e+07
8 10 2 0.1000 1.8700e+07
[ angles ]
1 2 3 2 120.00 390.00
1 2 4 2 120.00 390.00
1 5 6 2 120.00 390.00
1 5 7 2 120.00 390.00
1 8 9 2 120.00 390.00
1 8 10 2 120.00 390.00
3 2 4 2 120.00 445.00
6 5 7 2 120.00 445.00
9 8 10 2 120.00 445.00
2 1 5 2 120.00 670.00
5 1 8 2 120.00 670.00
8 1 2 2 120.00 670.00
[ pairs ]
; ai aj funct c0 c1
2 6 1 0.000000e+00 0.000000e+00
2 7 1 0.000000e+00 0.000000e+00
2 9 1 0.000000e+00 0.000000e+00
2 10 1 0.000000e+00 0.000000e+00
5 3 1 0.000000e+00 0.000000e+00
5 4 1 0.000000e+00 0.000000e+00
5 9 1 0.000000e+00 0.000000e+00
5 10 1 0.000000e+00 0.000000e+00
8 3 1 0.000000e+00 0.000000e+00
8 4 1 0.000000e+00 0.000000e+00
8 6 1 0.000000e+00 0.000000e+00
8 7 1 0.000000e+00 0.000000e+00
[ dihedrals ]
; ai aj ak al gromos type
2 1 5 6 1 180.000 33.5 2
2 1 5 7 1 180.000 33.5 2
2 1 8 9 1 180.000 33.5 2
2 1 8 10 1 180.000 33.5 2
5 1 2 3 1 180.000 33.5 2
5 1 2 4 1 180.000 33.5 2
5 1 8 9 1 180.000 33.5 2
5 1 8 10 1 180.000 33.5 2
8 1 2 3 1 180.000 33.5 2
8 1 2 4 1 180.000 33.5 2
Thank you
Regards
Zaved Hazarika
PhD Scholar
Dept.of Molecular Biology and Biotechnology
Tezpur University
India
Hi,
Presumably Gdm has atoms connected by three adjacent bonds that generally
have negative potential, and there's enough Gdm to make the total for the
system negative. It's generally a good idea to understand how the topology
you're using for Gdm works.
Mark
On Tue, Apr 10, 2018 at 2:23 PM <za...@tezu.ernet.in> wrote:
Dear Gromacs Users
I have simulated ricin in presence of GdmCl (1519 Gdm and 1519 Cl) with
gromos54a7 ff. Simulations have been performed for 100ns each at 298K,
350K and 450K.
The Average Coulomb-14 Energies are as follows:
ricin in water (298K) : 3.42E+04 (positive value)
ricin in water (350K) : 3.41E+04 (positive value)
ricin in water (450K) : 3.40E+04 (positive value)
ricin + GdmCl (298K) :-3.16E+06 (negative value)
ricin + GdmCl (350K) : -3.17E+06 (negative value)
ricin + GdmCl (450K) : -3.17E+06 (negative value)
Can anyone suggest me why there is a (10 to the power 10) fold
difference
of average Coulomb-14 energy of ricin in presence of water and ricin in
presence of GdmCl?
Thank You
Regards
Zaved
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